LAPOINTE.db. March 7, 2019

Transcription

1 LAPOINTE.db March 7, 2019 LAPOINTEACCNUM Map Manufacturer identifiers to Accession Numbers LAPOINTEACCNUM is an R object that contains mappings between a manufacturer s identifiers and manufacturers accessions. For chip packages such as this, the ACCNUM mapping comes directly from the manufacturer. This is different from other mappings which are mapped onto the probes via an Entrez Gene identifier. Each manufacturer identifier maps to a vector containing a GenBank accession number. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 x <- LAPOINTEACCNUM # Get the probe identifiers that are mapped to an ACCNUM # Get the ACCNUM for the first five probes 1

2 2 LAPOINTE.db LAPOINTEALIAS2PROBE Map between Common Gene Symbol Identifiers and Manufacturer Identifiers LAPOINTEALIAS is an R object that provides mappings between common gene symbol identifiers and manufacturer identifiers. Each gene symbol is mapped to a named vector of manufacturer identifiers. The name represents the gene symbol and the vector contains all manufacturer identifiers that are found for that symbol. An NA is reported for any gene symbol that cannot be mapped to any manufacturer identifiers. This mapping includes ALL gene symbols including those which are already listed in the SYMBOL map. The SYMBOL map is meant to only list official gene symbols, while the ALIAS maps are meant to store all used symbols. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 # Convert the object to a list xx <- as.list(lapointealias2probe) if(length(xx) > 0){ # Get the probe identifiers for the first two aliases xx[1:2] LAPOINTE.db Bioconductor annotation data package Welcome to the LAPOINTE.db annotation Package. The purpose of this package is to provide detailed information about the LAPOINTE platform. This package is updated biannually. Objects in this package are accessed using the select() interface. See?select in the AnnotationDbi package for details.

3 LAPOINTECHR 3 AnnotationDb-class for use of keys(), columns() and select(). columns(lapointe.db) ## The 'old style' of interacting with these objects is manipulation as ## bimaps. While this approach is still available we strongly encourage the ## use of select(). ls("package:lapointe.db") LAPOINTECHR Map Manufacturer IDs to Chromosomes LAPOINTECHR is an R object that provides mappings between a manufacturer identifier and the chromosome that contains the gene of interest. Each manufacturer identifier maps to a vector of chromosomes. Due to inconsistencies that may exist at the time the object was built, the vector may contain more than one chromosome (e.g., the identifier may map to more than one chromosome). If the chromosomal location is unknown, the vector will contain an NA. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 x <- LAPOINTECHR # Get the probe identifiers that are mapped to a chromosome # Get the CHR for the first five probes

4 4 LAPOINTECHRLOC LAPOINTECHRLENGTHS A named vector for the length of each of the chromosomes LAPOINTECHRLENGTHS provides the length measured in base pairs for each of the chromosomes. This is a named vector with chromosome numbers as the names and the corresponding lengths for chromosomes as the values. Total lengths of chromosomes were derived by calculating the number of base pairs on the sequence string for each chromosome. tt <- LAPOINTECHRLENGTHS # Length of chromosome 1 tt["1"] LAPOINTECHRLOC Map Manufacturer IDs to Chromosomal Location LAPOINTECHRLOC is an R object that maps manufacturer identifiers to the starting position of the gene. The position of a gene is measured as the number of base pairs. The CHRLOCEND mapping is the same as the CHRLOC mapping except that it specifies the ending base of a gene instead of the start.

5 LAPOINTEENSEMBL 5 Each manufacturer identifier maps to a named vector of chromosomal locations, where the name indicates the chromosome. Due to inconsistencies that may exist at the time the object was built, these vectors may contain more than one chromosome and/or location. If the chromosomal location is unknown, the vector will contain an NA. Chromosomal locations on both the sense and antisense strands are measured as the number of base pairs from the p (5 end of the sense strand) to q (3 end of the sense strand) arms. Chromosomal locations on the antisense strand have a leading "-" sign (e. g ). Since some genes have multiple start sites, this field can map to multiple locations. Mappings were based on data provided by: UCSC Genome Bioinformatics (Homo sapiens) ftp://hgdownload.cse.ucsc.edu With a date stamp from the source of: 2010-Mar22 x <- LAPOINTECHRLOC # Get the probe identifiers that are mapped to chromosome locations # Get the CHRLOC for the first five probes LAPOINTEENSEMBL Map Ensembl gene accession numbers with Entrez Gene identifiers LAPOINTEENSEMBL is an R object that contains mappings between manufacturer identifiers and Ensembl gene accession numbers. This object is a simple mapping of manufacturer identifiers to Ensembl gene Accession Numbers. Mappings were based on data provided by BOTH of these sources: biomart/martview/ ftp://ftp.ncbi.nlm.nih.gov/gene/data For most species, this mapping is a combination of manufacturer to ensembl IDs from BOTH NCBI and ensembl. Users who wish to only use mappings from NCBI are encouraged to see

6 6 LAPOINTEENTREZID the ncbi2ensembl table in the appropriate organism package. Users who wish to only use mappings from ensembl are encouraged to see the ensembl2ncbi table which is also found in the appropriate organism packages. These mappings are based upon the ensembl table which is contains data from BOTH of these sources in an effort to maximize the chances that you will find a match. For worms and flies however, this mapping is based only on sources from ensembl, as these organisms do not have ensembl to entrez gene mapping data at NCBI. x <- LAPOINTEENSEMBL # Get the entrez gene IDs that are mapped to an Ensembl ID mapped_genes <- mappedkeys(x) xx <- as.list(x[mapped_genes]) # Get the Ensembl gene IDs for the first five genes #For the reverse map ENSEMBL2PROBE: xx <- as.list(lapointeensembl2probe) if(length(xx) > 0){ # Gets the entrez gene IDs for the first five Ensembl IDs LAPOINTEENTREZID Map between Manufacturer Identifiers and Entrez Gene LAPOINTEENTREZID is an R object that provides mappings between manufacturer identifiers and Entrez Gene identifiers. Each manufacturer identifier is mapped to a vector of Entrez Gene identifiers. An NA is assigned to those manufacturer identifiers that can not be mapped to an Entrez Gene identifier at this time.

7 LAPOINTEENZYME 7 If a given manufacturer identifier can be mapped to different Entrez Gene identifiers from various sources, we attempt to select the common identifiers. If a concensus cannot be determined, we select the smallest identifier. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 References x <- LAPOINTEENTREZID # Get the probe identifiers that are mapped to an ENTREZ Gene ID # Get the ENTREZID for the first five probes LAPOINTEENZYME Maps between Manufacturer IDs and Enzyme Commission (EC) Numbers LAPOINTEENZYME is an R object that provides mappings between manufacturer identifiers and EC numbers. LAPOINTEENZYME2PROBE is an R object that maps Enzyme Commission (EC) numbers to manufacturer identifiers. When the LAPOINTEENZYME maping viewed as a list, each manufacturer identifier maps to a named vector containing the EC number that corresponds to the enzyme produced by that gene. The names corresponds to the manufacturer identifiers. If this information is unknown, the vector will contain an NA. For the LAPOINTEENZYME2PROBE, each EC number maps to a named vector containing all of the manufacturer identifiers that correspond to the gene that produces that enzyme. The name of the vector corresponds to the EC number.

8 8 LAPOINTEENZYME Enzyme Commission numbers are assigned by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology to allow enzymes to be identified. An Enzyme Commission number is of the format EC x.y.z.w, where x, y, z, and w are numeric numbers. In LAPOINTEENZYME2PROBE, EC is dropped from the Enzyme Commission numbers. Enzyme Commission numbers have corresponding names that describe the functions of enzymes in such a way that EC x is a more general description than EC x.y that in turn is a more general description than EC x.y.z. The top level EC numbers and names are listed below: EC 1 oxidoreductases EC 2 transferases EC 3 hydrolases EC 4 lyases EC 5 isomerases EC 6 ligases The EC name for a given EC number can be viewed at jcbn/index.html#6 Mappings between probe identifiers and enzyme identifiers were obtained using files provided by: KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15 References ftp://ftp.genome.ad.jp/pub/kegg/pathways x <- LAPOINTEENZYME # Get the probe identifiers that are mapped to an EC number # Get the ENZYME for the first five probes # Now convert LAPOINTEENZYME2PROBE to a list to see inside xx <- as.list(lapointeenzyme2probe) if(length(xx) > 0){ # Get the probe identifiers for the first five enzyme #commission numbers

9 LAPOINTEGENENAME 9 LAPOINTEGENENAME Map between Manufacturer IDs and Genes LAPOINTEGENENAME is an R object that maps manufacturer identifiers to the corresponding gene name. Each manufacturer identifier maps to a named vector containing the gene name. The vector name corresponds to the manufacturer identifier. If the gene name is unknown, the vector will contain an NA. Gene names currently include both the official (validated by a nomenclature committee) and preferred names (interim selected for display) for genes. Efforts are being made to differentiate the two by adding a name to the vector. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 x <- LAPOINTEGENENAME # Get the probe identifiers that are mapped to a gene name # Get the GENENAME for the first five probes

10 10 LAPOINTEGO LAPOINTEGO Maps between manufacturer IDs and Gene Ontology (GO) IDs LAPOINTEGO is an R object that provides mappings between manufacturer identifiers and the GO identifiers that they are directly associated with. This mapping and its reverse mapping (LA- POINTEGO2PROBE) do NOT associate the child terms from the GO ontology with the gene. Only the directly evidenced terms are represented here. LAPOINTEGO2ALLPROBES is an R object that provides mappings between a given GO identifier and all of the manufacturer identifiers annotated at that GO term OR TO ONE OF IT S CHILD NODES in the GO ontology. Thus, this mapping is much larger and more inclusive than LA- POINTEGO2PROBE. If LAPOINTEGO is cast as a list, each manufacturer identifier is mapped to a list of lists. The names on the outer list are GO identifiers. Each inner list consists of three named elements: GOID, Ontology, and Evidence. The GOID element matches the GO identifier named in the outer list and is included for convenience when processing the data using lapply. The Ontology element indicates which of the three Gene Ontology categories this identifier belongs to. The categories are biological process (BP), cellular component (CC), and molecular function (MF). The Evidence element contains a code indicating what kind of evidence supports the association of the GO identifier to the manufacturer id. Some of the evidence codes in use include: IMP: inferred from mutant phenotype IGI: inferred from genetic interaction IPI: inferred from physical interaction ISS: inferred from sequence similarity IDA: inferred from direct assay IEP: inferred from expression pattern IEA: inferred from electronic annotation TAS: traceable author statement NAS: non-traceable author statement ND: no biological data available IC: inferred by curator A more complete listing of evidence codes can be found at: If LAPOINTEGO2ALLPROBES or LAPOINTEGO2PROBE is cast as a list, each GO term maps to a named vector of manufacturer identifiers and evidence codes. A GO identifier may be mapped to the same manufacturer identifier more than once but the evidence code can be different. Mappings between Gene Ontology identifiers and Gene Ontology terms and other information are available in a separate data package named GO.

11 LAPOINTEGO 11 Whenever any of these mappings are cast as a data.frame, all the results will be output in an appropriate tabular form. Mappings between manufacturer identifiers and GO information were obtained through their mappings to manufacturer identifiers. NAs are assigned to manufacturer identifiers that can not be mapped to any Gene Ontology information. Mappings between Gene Ontology identifiers an Gene Ontology terms and other information are available in a separate data package named GO. All mappings were based on data provided by: Gene Ontology ftp://ftp.geneontology.org/pub/go/godatabase/archive/lates lite/ With a date stamp from the source of: References ftp://ftp.ncbi.nlm.nih.gov/gene/data/ LAPOINTEGO2ALLPROBES x <- LAPOINTEGO # Get the manufacturer identifiers that are mapped to a GO ID mapped_genes <- mappedkeys(x) xx <- as.list(x[mapped_genes]) # Try the first one got <- got[[1]][["goid"]] got[[1]][["ontology"]] got[[1]][["evidence"]] # For the reverse map: xx <- as.list(lapointego2probe) if(length(xx) > 0){ # Gets the manufacturer ids for the top 2nd and 3nd GO identifiers goids <- xx[2:3] # Gets the manufacturer ids for the first element of goids goids[[1]] # Evidence code for the mappings names(goids[[1]]) # Convert LAPOINTEGO2ALLPROBES to a list xx <- as.list(lapointego2allprobes) if(length(xx) > 0){ # Gets the manufacturer identifiers for the top 2nd and 3nd GO identifiers goids <- xx[2:3] # Gets all the manufacturer identifiers for the first element of goids goids[[1]]

12 12 LAPOINTEMAP # Evidence code for the mappings names(goids[[1]]) LAPOINTEMAP Map between Manufacturer Identifiers and cytogenetic maps/bands LAPOINTEMAP is an R object that provides mappings between manufacturer identifiers and cytoband locations. Each manufacturer identifier is mapped to a vector of cytoband locations. The vector length may be one or longer, if there are multiple reported chromosomal locations for a given gene. An NA is reported for any manufacturer identifiers that cannot be mapped to a cytoband at this time. Cytogenetic bands for most higher organisms are labeled p1, p2, p3, q1, q2, q3 (p and q are the p and q arms), etc., counting from the centromere out toward the telomeres. At higher resolutions, sub-bands can be seen within the bands. The sub-bands are also numbered from the centromere out toward the telomere. Thus, a label of 7q31.2 indicates that the band is on chromosome 7, q arm, band 3, sub-band 1, and sub-sub-band 2. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 References x <- LAPOINTEMAP # Get the probe identifiers that are mapped to any cytoband # Get the MAP for the first five probes

13 LAPOINTEMAPCOUNTS 13 LAPOINTEMAPCOUNTS Number of mapped keys for the maps in package LAPOINTE.db DEPRECATED. Counts in the MAPCOUNT table are out of sync and should not be used. LAPOINTEMAPCOUNTS provides the "map count" (i.e. the count of mapped keys) for each map in package LAPOINTE.db. DEPRECATED. Counts in the MAPCOUNT table are out of sync and should not be used. This "map count" information is precalculated and stored in the package annotation DB. This allows some quality control and is used by the checkmapcounts function defined in AnnotationDbi to compare and validate different methods (like count.mappedkeys(x) or sum(!is.na(as.list(x)))) for getting the "map count" of a given map. LAPOINTEOMIM Map between Manufacturer Identifiers and Mendelian Inheritance in Man (MIM) identifiers LAPOINTEOMIM is an R object that provides mappings between manufacturer identifiers and OMIM identifiers. Each manufacturer identifier is mapped to a vector of OMIM identifiers. The vector length may be one or longer, depending on how many OMIM identifiers the manufacturer identifier maps to. An NA is reported for any manufacturer identifier that cannot be mapped to an OMIM identifier at this time. OMIM is based upon the book Mendelian Inheritance in Man (V. A. McKusick) and focuses primarily on inherited or heritable genetic diseases. It contains textual information, pictures, and reference information that can be searched using various terms, among which the MIM number is one. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 References entrez/query.fcgi?db=omim

14 14 LAPOINTEORGANISM x <- LAPOINTEOMIM # Get the probe identifiers that are mapped to a OMIM ID # Get the OMIM for the first five probes LAPOINTEORGANISM The Organism information for LAPOINTE LAPOINTEORGANISM is an R object that contains a single item: a character string that names the organism for which LAPOINTE was built. LAPOINTEORGPKG is an R object that contains a chararcter vector with the name of the organism package that a chip package depends on for its gene-centric annotation. Although the package name is suggestive of the organism for which it was built, LAPOINTEOR- GANISM provides a simple way to programmatically extract the organism name. LAPOINTE- ORGPKG provides a simple way to programmatically extract the name of the parent organism package. The parent organism package is a strict dependency for chip packages as this is where the gene cetric information is ultimately extracted from. The full package name will always be this string plus the extension ".db". But most programatic acces will not require this extension, so its more convenient to leave it out. LAPOINTEORGANISM LAPOINTEORGPKG

15 LAPOINTEPATH 15 LAPOINTEPATH Mappings between probe identifiers and KEGG pathway identifiers KEGG (Kyoto Encyclopedia of Genes and Genomes) maintains pathway data for various organisms. LAPOINTEPATH maps probe identifiers to the identifiers used by KEGG for pathways in which the genes represented by the probe identifiers are involved LAPOINTEPATH2PROBE is an R object that provides mappings between KEGG identifiers and manufacturer identifiers. Each KEGG pathway has a name and identifier. Pathway name for a given pathway identifier can be obtained using the KEGG data package that can either be built using AnnBuilder or downloaded from Bioconductor Graphic presentations of pathways are searchable at url by using pathway identifiers as keys. Mappings were based on data provided by: KEGG GENOME ftp://ftp.genome.jp/pub/kegg/genomes With a date stamp from the source of: 2011-Mar15 References x <- LAPOINTEPATH # Get the probe identifiers that are mapped to a KEGG pathway ID # Get the PATH for the first five probes # Now convert the LAPOINTEPATH2PROBE object to a list xx <- as.list(lapointepath2probe) if(length(xx) > 0){

16 16 LAPOINTEPMID # Get the probe identifiers for the first two pathway identifiers xx[1:2] LAPOINTEPFAM Maps between Manufacturer Identifiers and PFAM Identifiers LAPOINTEPFAM is an R object that provides mappings between manufacturer identifiers and PFAM identifiers. The bimap interface for PFAM is defunct. Please use select() interface to PFAM identifiers. See?AnnotationDbi::select for details. LAPOINTEPMID Maps between Manufacturer Identifiers and PubMed Identifiers LAPOINTEPMID is an R object that provides mappings between manufacturer identifiers and PubMed identifiers. LAPOINTEPMID2PROBE is an R object that provides mappings between PubMed identifiers and manufacturer identifiers. When LAPOINTEPMID is viewed as a list each manufacturer identifier is mapped to a named vector of PubMed identifiers. The name associated with each vector corresponds to the manufacturer identifier. The length of the vector may be one or greater, depending on how many PubMed identifiers a given manufacturer identifier is mapped to. An NA is reported for any manufacturer identifier that cannot be mapped to a PubMed identifier. When LAPOINTEPMID2PROBE is viewed as a list each PubMed identifier is mapped to a named vector of manufacturer identifiers. The name represents the PubMed identifier and the vector contains all manufacturer identifiers that are represented by that PubMed identifier. The length of the vector may be one or longer, depending on how many manufacturer identifiers are mapped to a given PubMed identifier. Titles, abstracts, and possibly full texts of articles can be obtained from PubMed by providing a valid PubMed identifier. The pubmed function of annotate can also be used for the same purpose. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 References

17 LAPOINTEPROSITE 17 x <- LAPOINTEPMID # Get the probe identifiers that are mapped to any PubMed ID if(length(xx) > 0){ # Get the PubMed identifiers for the first two probe identifiers xx[1:2] if(interactive() &&!is.null() &&!is.na() && require(annotate)){ # Get article information as XML files xmls <- pubmed(, disp = "data") # View article information using a browser pubmed(, disp = "browser") # Now convert the reverse map object LAPOINTEPMID2PROBE to a list xx <- as.list(lapointepmid2probe) if(length(xx) > 0){ # Get the probe identifiers for the first two PubMed identifiers xx[1:2] if(interactive() && require(annotate)){ # Get article information as XML files for a PubMed id xmls <- pubmed(names(xx)[1], disp = "data") # View article information using a browser pubmed(names(xx)[1], disp = "browser") LAPOINTEPROSITE Maps between Manufacturer Identifiers and PROSITE Identifiers LAPOINTEPROSITE is an R object that provides mappings between manufacturer identifiers and PROSITE identifiers.

18 18 LAPOINTEREFSEQ The bimap interface for PROSITE is defunct. Please use select() interface to PROSITE identifiers. See?AnnotationDbi::select for details. LAPOINTEREFSEQ Map between Manufacturer Identifiers and RefSeq Identifiers LAPOINTEREFSEQ is an R object that provides mappings between manufacturer identifiers and RefSeq identifiers. Each manufacturer identifier is mapped to a named vector of RefSeq identifiers. The name represents the manufacturer identifier and the vector contains all RefSeq identifiers that can be mapped to that manufacturer identifier. The length of the vector may be one or greater, depending on how many RefSeq identifiers a given manufacturer identifier can be mapped to. An NA is reported for any manufacturer identifier that cannot be mapped to a RefSeq identifier at this time. RefSeq identifiers differ in format according to the type of record the identifiers are for as shown below: NG\_XXXXX: RefSeq accessions for genomic region (nucleotide) records NM\_XXXXX: RefSeq accessions for mrna records NC\_XXXXX: RefSeq accessions for chromosome records NP\_XXXXX: RefSeq accessions for protein records XR\_XXXXX: RefSeq accessions for model RNAs that are not associated with protein products XM\_XXXXX: RefSeq accessions for model mrna records XP\_XXXXX: RefSeq accessions for model protein records Where XXXXX is a sequence of integers. NCBI allows users to query the RefSeq database using RefSeq identifiers. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 References

19 LAPOINTESYMBOL 19 x <- LAPOINTEREFSEQ # Get the probe identifiers that are mapped to any RefSeq ID # Get the REFSEQ for the first five probes LAPOINTESYMBOL Map between Manufacturer Identifiers and Gene Symbols LAPOINTESYMBOL is an R object that provides mappings between manufacturer identifiers and gene abbreviations. Each manufacturer identifier is mapped to an abbreviation for the corresponding gene. An NA is reported if there is no known abbreviation for a given gene. Symbols typically consist of 3 letters that define either a single gene (ABC) or multiple genes (ABC1, ABC2, ABC3). Gene symbols can be used as key words to query public databases such as Entrez Gene. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 References x <- LAPOINTESYMBOL

20 20 LAPOINTEUNIGENE # Get the probe identifiers that are mapped to a gene symbol # Get the SYMBOL for the first five probes LAPOINTEUNIGENE Map between Manufacturer Identifiers and UniGene cluster identifiers LAPOINTEUNIGENE is an R object that provides mappings between manufacturer identifiers and UniGene identifiers. Each manufacturer identifier is mapped to a UniGene identifier. An NA is reported if the manufacturer identifier cannot be mapped to UniGene at this time. A UniGene identifier represents a cluster of sequences of a gene. Using UniGene identifiers one can query the UniGene database for information about the sequences or the Entrez Gene database for information about the genes. Mappings were based on data provided by: Entrez Gene ftp://ftp.ncbi.nlm.nih.gov/gene/data With a date stamp from the source of: 2015-Sep27 References x <- LAPOINTEUNIGENE # Get the probe identifiers that are mapped to an UNIGENE ID # Get the UNIGENE for the first five probes

21 LAPOINTEUNIPROT 21 LAPOINTEUNIPROT Map Uniprot accession numbers with Entrez Gene identifiers LAPOINTEUNIPROT is an R object that contains mappings between the manufacturer identifiers and Uniprot accession numbers. This object is a simple mapping of manufacturer identifiers to Uniprot Accessions. Mappings were based on data provided by NCBI (link above) with an exception for fly, which required retrieving the data from ensembl x <- LAPOINTEUNIPROT # Get the entrez gene IDs that are mapped to an Uniprot ID mapped_genes <- mappedkeys(x) xx <- as.list(x[mapped_genes]) # Get the Uniprot IDs for the first five genes LAPOINTE_dbconn Collect information about the package annotation DB Some convenience functions for getting a connection object to (or collecting information about) the package annotation DB.

22 22 LAPOINTE_dbconn Usage Arguments LAPOINTE_dbconn() LAPOINTE_dbfile() LAPOINTE_dbschema(file="", show.indices=false) LAPOINTE_dbInfo() file show.indices A connection, or a character string naming the file to print to (see the file argument of the cat function for the details). The CREATE INDEX statements are not shown by default. Use show.indices=true to get them. Value LAPOINTE_dbconn returns a connection object to the package annotation DB. IMPORTANT: Don t call dbdisconnect on the connection object returned by LAPOINTE_dbconn or you will break all the AnnDbObj objects defined in this package! LAPOINTE_dbfile returns the path (character string) to the package annotation DB (this is an SQLite file). LAPOINTE_dbschema prints the schema definition of the package annotation DB. LAPOINTE_dbInfo prints other information about the package annotation DB. LAPOINTE_dbconn: a DBIConnection object representing an open connection to the package annotation DB. LAPOINTE_dbfile: a character string with the path to the package annotation DB. LAPOINTE_dbschema: none (invisible NULL). LAPOINTE_dbInfo: none (invisible NULL). dbgetquery, dbconnect, dbconn, dbfile, dbschema, dbinfo library(dbi) ## Count the number of rows in the "probes" table: dbgetquery(lapointe_dbconn(), "SELECT COUNT(*) FROM probes") LAPOINTE_dbschema() LAPOINTE_dbInfo()

23 Index Topic datasets LAPOINTE.db, 2 LAPOINTE_dbconn, 21 LAPOINTEACCNUM, 1 LAPOINTEALIAS2PROBE, 2 LAPOINTECHR, 3 LAPOINTECHRLENGTHS, 4 LAPOINTECHRLOC, 4 LAPOINTEENSEMBL, 5 LAPOINTEENTREZID, 6 LAPOINTEENZYME, 7 LAPOINTEGENENAME, 9 LAPOINTEGO, 10 LAPOINTEMAP, 12 LAPOINTEMAPCOUNTS, 13 LAPOINTEOMIM, 13 LAPOINTEORGANISM, 14 LAPOINTEPATH, 15 LAPOINTEPFAM, 16 LAPOINTEPMID, 16 LAPOINTEPROSITE, 17 LAPOINTEREFSEQ, 18 LAPOINTESYMBOL, 19 LAPOINTEUNIGENE, 20 LAPOINTEUNIPROT, 21 Topic utilities LAPOINTE_dbconn, 21 AnnDbObj, 22 cat, 22 checkmapcounts, 13 dbconn, 22 dbconnect, 22 dbdisconnect, 22 dbfile, 22 dbgetquery, 22 dbinfo, 22 dbschema, 22 LAPOINTE_dbfile (LAPOINTE_dbconn), 21 LAPOINTE_dbInfo (LAPOINTE_dbconn), 21 LAPOINTE_dbschema (LAPOINTE_dbconn), 21 LAPOINTEACCNUM, 1 LAPOINTEALIAS2PROBE, 2 LAPOINTECHR, 3 LAPOINTECHRLENGTHS, 4 LAPOINTECHRLOC, 4 LAPOINTECHRLOCEND (LAPOINTECHRLOC), 4 LAPOINTEENSEMBL, 5 LAPOINTEENSEMBL2PROBE (LAPOINTEENSEMBL), 5 LAPOINTEENTREZID, 6 LAPOINTEENZYME, 7 LAPOINTEENZYME2PROBE (LAPOINTEENZYME), 7 LAPOINTEGENENAME, 9 LAPOINTEGO, 10 LAPOINTEGO2ALLPROBES, 11 LAPOINTEGO2ALLPROBES (LAPOINTEGO), 10 LAPOINTEGO2PROBE (LAPOINTEGO), 10 LAPOINTELOCUSID (LAPOINTEENTREZID), 6 LAPOINTEMAP, 12 LAPOINTEMAPCOUNTS, 13 LAPOINTEOMIM, 13 LAPOINTEORGANISM, 14 LAPOINTEORGPKG (LAPOINTEORGANISM), 14 LAPOINTEPATH, 15 LAPOINTEPATH2PROBE (LAPOINTEPATH), 15 LAPOINTEPFAM, 16 LAPOINTEPMID, 16 LAPOINTEPMID2PROBE (LAPOINTEPMID), 16 LAPOINTEPROSITE, 17 LAPOINTEREFSEQ, 18 LAPOINTESYMBOL, 19 LAPOINTEUNIGENE, 20 LAPOINTEUNIPROT, 21 LAPOINTEUNIPROT2PROBE (LAPOINTEUNIPROT), 21 LAPOINTE (LAPOINTE.db), 2 LAPOINTE.db, 2 LAPOINTE_dbconn, 21 23